{"entity": "journal", "iuid": "0c50efa64a5a49c4bb030c3a0e1b4e3d", "timestamp": "2026-07-19T05:47:52.720Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/NPLANTS.json"}, "display": {"href": "https://publications.scilifelab.se/journal/NPLANTS"}}, "title": "NPLANTS", "issn": "2055-0278", "issn-l": "2055-0278", "publications_count": 9, "publications": [{"entity": "publication", "iuid": "5e3de96d3dfe4cc0bd7ab308e2adbcb9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e3de96d3dfe4cc0bd7ab308e2adbcb9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e3de96d3dfe4cc0bd7ab308e2adbcb9"}}, "title": "A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing.", "authors": [{"family": "Feng", "given": "Ming", "initials": "M", "orcid": "0000-0002-1690-5651", "researcher": {"href": "https://publications.scilifelab.se/researcher/8523b6aee63c4e76ac584692da4d7779.json"}}, {"family": "Zhang", "given": "Ai", "initials": "A", "orcid": "0000-0002-8308-9973", "researcher": {"href": "https://publications.scilifelab.se/researcher/a56072abd97148cf87466ad568502b83.json"}}, {"family": "Nguyen", "given": "Van", "initials": "V"}, {"family": "Bisht", "given": "Anchal", "initials": "A"}, {"family": "Almqvist", "given": "Curt", "initials": "C", "orcid": "0000-0001-5739-4854", "researcher": {"href": "https://publications.scilifelab.se/researcher/95e0d8e8446849dbbad0e7bbdcc53c06.json"}}, {"family": "De Veylder", "given": "Lieven", "initials": "L", "orcid": "0000-0003-1150-4426", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e15711bd16e4c0c8b20c1c26e581d77.json"}}, {"family": "Carlsbecker", "given": "Annelie", "initials": "A", "orcid": "0000-0002-8450-3718", "researcher": {"href": "https://publications.scilifelab.se/researcher/f913d526d4ea46b5bdd3f8bce6db1220.json"}}, {"family": "Melnyk", "given": "Charles W", "initials": "CW", "orcid": "0000-0003-3251-800X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd60bb90f97b42ca902c63ca66fbc96f.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "NPLANTS", "issn": "2055-0278", "volume": "10", "issue": "1", "pages": "53-65", "issn-l": "2055-0278"}, "abstract": "The widespread use of plant grafting enables eudicots and gymnosperms to join with closely related species and grow as one. Gymnosperms have dominated forests for over 200 million years, and despite their economic and ecological relevance, we know little about how they graft. Here we developed a micrografting method in conifers using young tissues that allowed efficient grafting with closely related species and between distantly related genera. Conifer graft junctions rapidly connected vasculature and differentially expressed thousands of genes including auxin and cell-wall-related genes. By comparing these genes to those induced during Arabidopsis thaliana graft formation, we found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis in Norway spruce (Picea abies) predicted that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a core regulator of graft healing. This gene was strongly up-regulated during both spruce and Arabidopsis grafting, and Arabidopsis mutants lacking PAT genes failed to attach tissues or successfully graft. Complementing Arabidopsis PAT mutants with the spruce PAT1 homolog rescued tissue attachment and enhanced callus formation. Together, our data show an ability for young tissues to graft with distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration.", "doi": "10.1038/s41477-023-01568-w", "pmid": "38168607", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10808061"}, {"db": "pii", "key": "10.1038/s41477-023-01568-w"}], "notes": [], "created": "2024-11-25T10:18:30.723Z", "modified": "2025-02-28T14:14:57.234Z"}, {"entity": "publication", "iuid": "c2cb0bab4db649efac151742b39cf0bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2cb0bab4db649efac151742b39cf0bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2cb0bab4db649efac151742b39cf0bb"}}, "title": "Auxin export from proximal fruits drives arrest in temporally competent inflorescences", "authors": [{"family": "Ware", "given": "Alexander", "initials": "A"}, {"family": "Walker", "given": "Catriona H", "initials": "CH", "orcid": "0000-0001-7854-4348", "researcher": {"href": "https://publications.scilifelab.se/researcher/37ada8225d8e4931b1d093af5a71306e.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Gonz\u00e1lez-Su\u00e1rez", "given": "Pablo", "initials": "P", "orcid": "0000-0002-2122-5984", "researcher": {"href": "https://publications.scilifelab.se/researcher/770ac95b3e6c44e28967de3fb8fbe149.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Bishopp", "given": "Anthony", "initials": "A"}, {"family": "Wilson", "given": "Zoe A", "initials": "ZA", "orcid": "0000-0003-0948-8770", "researcher": {"href": "https://publications.scilifelab.se/researcher/76cb7bfa2b1c4961ad52a2080f7c9822.json"}}, {"family": "Bennett", "given": "Tom", "initials": "T", "orcid": "0000-0003-1612-4019", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39f318b0f094229aa34d1c137575d6b.json"}}], "type": "journal-article", "published": "2020-05-25", "journal": {"title": "NPLANTS", "issn": "2055-0278", "issn-l": "2055-0278", "volume": "6", "issue": "6", "pages": "699-707"}, "abstract": "A well-defined set of regulatory pathways control entry into the reproductive phase in flowering plants, but little is known about the mechanistic control of the end-of-flowering despite this being a critical process for optimization of fruit and seed production. Complete fruit removal, or lack of fertile fruit-set, prevents timely inflorescence arrest in Arabidopsis, leading to a previous proposal that a cumulative fruit/seed-derived signal causes simultaneous 'global proliferative arrest'. Recent studies have suggested that inflorescence arrest involves gene expression changes in the inflorescence meristem that are, at least in part, controlled by the FRUITFULL-APETALA2 pathway; however, there is limited understanding of how this process is coordinated at the whole-plant level. Here, we provide a framework for the communication previously inferred in the global proliferative arrest model. We show that the end-of-flowering in Arabidopsis is not 'global' and does not occur synchronously between branches, but rather that the arrest of each inflorescence is a local process, driven by auxin export from fruit proximal to the inflorescence apex. Furthermore, we show that inflorescences are competent for arrest only once they reach a certain developmental age. Understanding the regulation of inflorescence arrest will be of major importance to extending and maximizing crop yields.", "doi": "10.1038/s41477-020-0661-z", "pmid": "32451444", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-020-0661-z"}], "notes": [], "created": "2020-01-21T10:14:13.466Z", "modified": "2025-10-17T13:03:16.780Z"}, {"entity": "publication", "iuid": "b7650f46ca4f4c56a430894a420c5bb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7650f46ca4f4c56a430894a420c5bb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7650f46ca4f4c56a430894a420c5bb3"}}, "title": "Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly.", "authors": [{"family": "Chen", "given": "Ming", "initials": "M"}, {"family": "Perez-Boerema", "given": "Annemarie", "initials": "A", "orcid": "0000-0002-1180-5838", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a711071c6844bdcb4c151971774435f.json"}}, {"family": "Zhang", "given": "Laixing", "initials": "L", "orcid": "0000-0001-9552-3848", "researcher": {"href": "https://publications.scilifelab.se/researcher/e60e16efc7454a6ebdf8697e9f51a03b.json"}}, {"family": "Li", "given": "Yanxue", "initials": "Y"}, {"family": "Yang", "given": "Maojun", "initials": "M", "orcid": "0000-0002-6798-3094", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2e4673b1b6f484990b2818076942f61.json"}}, {"family": "Li", "given": "Shizhong", "initials": "S", "orcid": "0000-0001-9605-1109", "researcher": {"href": "https://publications.scilifelab.se/researcher/df1330d71677410887cc6dcb0186355f.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"volume": "6", "issn": "2055-0278", "issue": "3", "pages": "314-320", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from the cyanobacterium Anabaena. This revealed a disrupted trimerization domain due to lack of the terminal residues of PsaL in the lumen, which resulted in PSI dimers with loose connections between monomers and weaker energy-coupled chlorophylls than in the trimer. At the dimer surface, specific phospholipids, cofactors and interactions in combination facilitated recruitment of another dimer to form a tetramer. Taken together, the relaxed luminal connections and lipid specificity at the dimer interface account for membrane curvature. PSI tetramer assembly appears to increase the surface area of the thylakoid membrane, which would contribute to PSI crowding.", "doi": "10.1038/s41477-020-0610-x", "pmid": "32170279", "labels": {"Cryo-EM": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-020-0610-x"}], "notes": [], "created": "2020-03-10T11:55:25.538Z", "modified": "2021-11-10T12:53:09.684Z"}, {"entity": "publication", "iuid": "cc640c9f07fa4f81aa6ecd3aa9fdf7df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc640c9f07fa4f81aa6ecd3aa9fdf7df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc640c9f07fa4f81aa6ecd3aa9fdf7df"}}, "title": "Structure of a minimal photosystem I from the green alga Dunaliella salina.", "authors": [{"family": "Perez-Boerema", "given": "Annemarie", "initials": "A", "orcid": "0000-0002-1180-5838", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a711071c6844bdcb4c151971774435f.json"}}, {"family": "Klaiman", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3807-6591", "researcher": {"href": "https://publications.scilifelab.se/researcher/37d495f21e6f4d9f8ef482f80ba11442.json"}}, {"family": "Caspy", "given": "Ido", "initials": "I", "orcid": "0000-0003-1981-1017", "researcher": {"href": "https://publications.scilifelab.se/researcher/a61b089ee32c4d9088ce16e1603ebcce.json"}}, {"family": "Netzer-El", "given": "Sigal Y", "initials": "SY"}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Nelson", "given": "Nathan", "initials": "N", "orcid": "0000-0003-3588-7265", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbfaea6e08764d5ba01172f6f2b01030.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"volume": "6", "issn": "2055-0278", "issue": "3", "pages": "321-327", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular complexes that contain core and peripheral antennae with multiple pigments. The structure of photosystem I (PSI) comprises the core and light-harvesting (LHCI) complexes, which together form PSI-LHCI. Here we determined the structure of PSI-LHCI from the salt-tolerant green alga Dunaliella salina using X-ray crystallography and electron cryo-microscopy. Our results reveal a previously undescribed configuration of the PSI core. It is composed of only 7 subunits, compared with 14-16 subunits in plants and the alga Chlamydomonas reinhardtii, and forms the smallest known PSI. The LHCI is poorly conserved at the sequence level and binds to pigments that form new energy pathways, and the interactions between the individual Lhca1-4 proteins are weakened. Overall, the data indicate the PSI of D. salina represents a different type of the molecular organization that provides important information for reconstructing the plasticity and evolution of PSI.", "doi": "10.1038/s41477-020-0611-9", "pmid": "32123351", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-020-0611-9"}], "notes": [], "created": "2020-03-10T11:57:34.902Z", "modified": "2021-11-10T12:53:30.915Z"}, {"entity": "publication", "iuid": "f496a5ada24c4f0cb2787a64d90492f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f496a5ada24c4f0cb2787a64d90492f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f496a5ada24c4f0cb2787a64d90492f9"}}, "title": "PIN-driven auxin transport emerged early in streptophyte evolution.", "authors": [{"family": "Skokan", "given": "Roman", "initials": "R", "orcid": "0000-0003-0467-0792", "researcher": {"href": "https://publications.scilifelab.se/researcher/455acda9a8094e7f9d621e7036e0f388.json"}}, {"family": "Medveck\u00e1", "given": "Eva", "initials": "E"}, {"family": "Viaene", "given": "Tom", "initials": "T"}, {"family": "Vosolsob\u011b", "given": "Stanislav", "initials": "S"}, {"family": "Zwiewka", "given": "Marta", "initials": "M"}, {"family": "M\u00fcller", "given": "Karel", "initials": "K"}, {"family": "Sk\u016fpa", "given": "Petr", "initials": "P"}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Zhang", "given": "Yuzhou", "initials": "Y"}, {"family": "Janacek", "given": "Dorina P", "initials": "DP"}, {"family": "Hammes", "given": "Ulrich Z", "initials": "UZ"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Nodzy\u0144ski", "given": "Tomasz", "initials": "T"}, {"family": "Petr\u00e1\u0161ek", "given": "Jan", "initials": "J"}, {"family": "Friml", "given": "Ji\u0159\u00ed", "initials": "J", "orcid": "0000-0002-8302-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e525fe6afc5490a86223e38be195cee.json"}}], "type": "journal article", "published": "2019-11-00", "journal": {"title": "NPLANTS", "issn": "2055-0278", "volume": "5", "issue": "11", "pages": "1114-1119", "issn-l": "2055-0278"}, "abstract": "PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.", "doi": "10.1038/s41477-019-0542-5", "pmid": "31712756", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-019-0542-5"}], "notes": [], "created": "2020-01-07T15:51:45.627Z", "modified": "2025-10-17T13:03:17.274Z"}, {"entity": "publication", "iuid": "9e64fa647d38400ba492319e0a977640", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e64fa647d38400ba492319e0a977640.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e64fa647d38400ba492319e0a977640"}}, "title": "Paternally expressed imprinted genes associate with hybridization barriers in Capsella", "authors": [{"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Hatorangan", "given": "Marcelinus R", "initials": "MR"}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Cornille", "given": "Amandine", "initials": "A"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}], "type": "journal-article", "published": "2018-06-00", "journal": {"volume": "4", "issn": "2055-0278", "issue": "6", "pages": "352-357", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": null, "doi": "10.1038/s41477-018-0161-6", "pmid": "29808019", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GEO", "description": null, "key": "GSE103209"}], "notes": [], "created": "2018-09-14T11:54:00.459Z", "modified": "2024-01-16T13:48:46.176Z"}, {"entity": "publication", "iuid": "0e147a5dedd845faac46f7a0cdbb4de5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e147a5dedd845faac46f7a0cdbb4de5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e147a5dedd845faac46f7a0cdbb4de5"}}, "title": "Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor", "authors": [{"family": "Perez Boerema", "given": "Annemarie", "initials": "A"}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Paul", "given": "Bijoya", "initials": "B"}, {"family": "Tobiasson", "given": "Victor", "initials": "V", "orcid": "0000-0001-8920-017X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5208789057a94d0d9575476bf9c88d5a.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5434ab128e04b2b951abbbea77221c8.json"}}, {"family": "Wallden", "given": "Karin", "initials": "K"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Amunts", "given": "A", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal-article", "published": "2018-04-02", "journal": {"volume": "4", "issn": "2055-0278", "issue": "4", "pages": "212-217", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome1,2. Despite recent structural information3-6, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 \u00c5 resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.", "doi": "10.1038/s41477-018-0129-6", "pmid": "29610536", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-018-0129-6"}], "notes": [], "created": "2018-04-11T08:19:19.613Z", "modified": "2023-12-04T10:12:49.407Z"}, {"entity": "publication", "iuid": "788bcedf458c46bca3f4b731190d6c65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65"}}, "title": "Spatially resolved transcriptome profiling in model plant species.", "authors": [{"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Navarro", "given": "Jos\u00e9 Fernandez", "initials": "JF"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "McKee", "given": "Lauren S", "initials": "LS"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Bulone", "given": "Vincent", "initials": "V"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2017-05-08", "journal": {"volume": "3", "issn": "2055-0278", "issue": null, "pages": "17061", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.", "doi": "10.1038/nplants.2017.61", "pmid": "28481330", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nplants201761"}], "notes": [], "created": "2017-08-23T14:09:59.506Z", "modified": "2024-01-16T13:48:47.983Z"}, {"entity": "publication", "iuid": "b8c51f425fe94bbbb65abb8767b49924", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8c51f425fe94bbbb65abb8767b49924.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8c51f425fe94bbbb65abb8767b49924"}}, "title": "Local auxin metabolism regulates environment-induced hypocotyl elongation", "authors": [{"family": "Zheng", "given": "Zuyu", "initials": "Z"}, {"family": "Guo", "given": "Yongxia", "initials": "Y"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Chen", "given": "William", "initials": "W"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Noel", "given": "Joseph P", "initials": "JP"}, {"family": "Chory", "given": "Joanne", "initials": "J"}], "type": "journal-article", "published": "2016-03-21", "journal": {"volume": "2", "issn": "2055-0278", "issue": "4", "pages": "16025", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": null, "doi": "10.1038/nplants.2016.25", "pmid": "27249562", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T12:40:59.266Z", "modified": "2025-10-17T13:03:19.692Z"}], "created": "2017-08-23T14:09:59.514Z", "modified": "2020-11-27T13:14:08.968Z"}